package compbio.cassandra;
import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.EOFException;
+import java.io.FileNotFoundException;
import java.io.IOException;
+import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import compbio.cassandra.JpredParser;
public class JpredParserHTTP implements JpredParser {
- private CassandraCreate cc = new CassandraCreate();
+ private CassandraWriter cw = new CassandraWriter();
private String dirprefix;
-
- JpredParserHTTP() {
- this.dirprefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
+ private List<FastaSequence> alignment;
+ private List<FastaSequence> predictions;
+ private int countNoData;
+
+ public JpredParserHTTP() {
+ dirprefix = "http://www.compbio.dundee.ac.uk/www-jpred/results";
}
-
- JpredParserHTTP(String sourceurl) {
- this.dirprefix = sourceurl;
+
+ public JpredParserHTTP(String sourceurl) {
+ dirprefix = sourceurl;
}
- public void setSource (String newsourceprefix) {
- this.dirprefix = newsourceprefix;
+ public void setSource(String newsourceprefix) {
+ dirprefix = newsourceprefix;
}
- public void Parsing(String source, int nDays) {
+ public void Parsing(String source, int nDays) throws IOException {
Calendar cal = Calendar.getInstance();
cal.add(Calendar.DATE, -nDays);
for (int i = 0; i < nDays; ++i) {
}
}
+ /*
+ * The method parses the Jpred output concise file in the FASTA format If
+ * there is a record with ID = QUERY or jobid, this a "one protein" job
+ * otherwise this is an alignment job
+ */
+ private String parsePredictions(final InputStream stream, String jobid) throws FileNotFoundException {
+ final FastaReader fr = new FastaReader(stream);
+ String protein = "";
+ alignment = new ArrayList<FastaSequence>();
+ predictions = new ArrayList<FastaSequence>();
+ while (fr.hasNext()) {
+ final FastaSequence fs = fr.next();
+ String seqid = fs.getId();
+ String seq = fs.getSequence().replaceAll("\n", "");
+ if (seqid.equals("jnetpred") || seqid.equals("Lupas_21") || seqid.equals("Lupas_14") || seqid.equals("Lupas_28")
+ || seqid.equals("JNETSOL25") || seqid.equals("JNETSOL5") || seqid.equals("JNETSOL0") || seqid.equals("JNETCONF")
+ || seqid.equals("JNETHMM") || seqid.equals("JNETPSSM") || seqid.equals("JNETCONF")) {
+ predictions.add(fs);
+ } else {
+ alignment.add(fs);
+ if (seqid.equals("QUERY") || seqid.equals(jobid))
+ protein = seq;
+ }
+ }
+ return protein;
+ }
+
+ private String parseLogFile(final InputStream stream) throws IOException {
+ String out = "";
+ BufferedReader buffer = new BufferedReader(new InputStreamReader(stream));
+ String line;
+ while (null != (line = buffer.readLine())) {
+ out += line;
+ }
+ return out;
+ }
+
+ private List<Byte> parseArchiveFile(final InputStream stream) throws IOException {
+ DataInputStream data_in = new DataInputStream(stream);
+ List<Byte> out = new ArrayList<Byte>();
+ while (true) {
+ try {
+ out.add(data_in.readByte());
+ } catch (EOFException eof) {
+ break;
+ }
+ }
+ return out;
+ }
+
+ private int analyseJob(String[] job) throws IOException {
+ boolean running = true;
+ boolean ConcisefileExists = false;
+ boolean LogfileExists = false;
+ String id = job[job.length - 1];
+ String startdatestring = job[0].substring(0, job[0].indexOf(":"));
+ Date startdate = new Date(0);
+ Date starttime = new Date(0);
+ Date endtime = new Date(0);
+ Date currDate = new Date();
+ String ip = job[2];
+ String execstatus = "OK";
+ String finalstatus = "OK";
+ String protein = "";
+ long exectime = 0;
+ String log = "";
+ String maindir = dirprefix + "/" + id + "/";
+ String concisefile = dirprefix + "/" + id + "/" + id + ".concise.fasta";
+ String archivefile = dirprefix + "/" + id + "/" + id + ".tar.gz";
+ String logfile = dirprefix + "/" + id + "/LOG";
+ SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
+ SimpleDateFormat timeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s");
+ try {
+ startdate = dateformatter.parse(startdatestring);
+ starttime = timeformatter.parse(job[0]);
+ endtime = timeformatter.parse(job[1]);
+ exectime = (endtime.getTime() - starttime.getTime()) / 1000;
+ } catch (ParseException e) {
+ e.printStackTrace();
+ }
+
+ try {
+ URL dirurl = new URL(maindir);
+ HttpURLConnection httpConnection_dirurl = (HttpURLConnection) dirurl.openConnection();
+ if (httpConnection_dirurl.getResponseCode() < 199 || 300 <= httpConnection_dirurl.getResponseCode()) {
+ return 0;
+ }
+ URL conciseurl = new URL(concisefile);
+ URL archiveurl = new URL(archivefile);
+ URL logurl = new URL(logfile);
+ HttpURLConnection httpConnection_conciseurl = (HttpURLConnection) conciseurl.openConnection();
+ HttpURLConnection httpConnection_logurl = (HttpURLConnection) logurl.openConnection();
+ HttpURLConnection httpConnection_archiveurl = (HttpURLConnection) archiveurl.openConnection();
+ if (199 < httpConnection_conciseurl.getResponseCode() && httpConnection_conciseurl.getResponseCode() < 300) {
+ ConcisefileExists = true;
+ running = false;
+ try {
+ protein = parsePredictions(conciseurl.openStream(), id);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ } else {
+ // The job still can be running of failed...
+ ++countNoData;
+ alignment = new ArrayList<FastaSequence>();
+ predictions = new ArrayList<FastaSequence>();
+ }
+ if (199 < httpConnection_logurl.getResponseCode() && httpConnection_logurl.getResponseCode() < 300) {
+ LogfileExists = true;
+ log = parseLogFile(logurl.openStream());
+ } else {
+ // The job has not been started at all...
+ execstatus = "FAIL";
+ finalstatus = "STOPPED";
+ running = false;
+ }
+ if (log.matches("(.*)TIMEOUT\\syour\\sjob\\stimed\\sout(.*)")) {
+ // blast job was too long (more than 3600 secs by default)...
+ execstatus = "FAIL";
+ finalstatus = "TIMEDOUT";
+ running = false;
+ } else if (log.matches("(.*)Jpred\\serror:\\sDied\\sat(.*)")) {
+ // an internal Jpred error...
+ execstatus = "FAIL";
+ finalstatus = "JPREDERROR";
+ running = false;
+ } else if ((currDate.getTime() - endtime.getTime()) / 1000 > 3601 && LogfileExists && !ConcisefileExists) {
+ // the job was stopped with unknown reason...
+ execstatus = "FAIL";
+ finalstatus = "STOPPED";
+ running = false;
+ }
+
+ httpConnection_conciseurl.disconnect();
+ httpConnection_logurl.disconnect();
+ httpConnection_archiveurl.disconnect();
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ }
+
+ if (!running) {
+ long t = startdate.getTime();
+ cw.FormQueryTables(t, job[0], job[1], ip, id, execstatus, finalstatus, protein, predictions);
+ cw.ArchiveData(t, exectime, ip, id, execstatus, finalstatus, protein, predictions, alignment, log, archivefile);
+ return 1;
+ } else
+ System.out.println("job " + id + " is running");
+
+ return 0;
+ }
+
private void ParsingForDate(String input, String date) {
int totalcount = 0;
- int countNoData = 0;
- int countUnclearFASTAid = 0;
int countinsertions = 0;
int countinserted = 0;
- int counAlignments = 0;
- int countStrange = 0;
+ int countNotanalyzed = 0;
+ countNoData = 0;
System.out.println("Inserting jobs for " + date);
try {
String line;
while ((line = alljobs.readLine()) != null) {
- if (line.matches(date + "(.*)jp_[^\\s]+")) {
- String[] table = line.split("\\s+");
- String id = table[table.length - 1];
+ if (line.matches(date + ":(.*)jp_[^\\s]+")) {
totalcount++;
- if (!cc.CheckID(id)) {
- URL urltable = new URL(dirprefix + "/" + id + "/" + id + ".concise.fasta");
- HttpURLConnection httpConnection = (HttpURLConnection) urltable.openConnection();
- int responsecode = httpConnection.getResponseCode();
- if (199 < responsecode && responsecode < 300) {
- try {
- final FastaReader fr = new FastaReader(urltable.openStream());
- final List<FastaSequence> seqs = new ArrayList<FastaSequence>();
- String newprotein = "";
- while (fr.hasNext()) {
- final FastaSequence fs = fr.next();
- if (fs.getId().equals("QUERY") || fs.getId().equals(id))
- newprotein = fs.getSequence().replaceAll("\n", "");
- else
- seqs.add(fs);
- }
- if (newprotein.equals("")) {
- countUnclearFASTAid++;
- } else {
- SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
- String dateInString1 = table[0].substring(0, table[0].indexOf(":"));
- long dateWork1 = 0;
- try {
- Date dat1 = formatter.parse(dateInString1);
- dateWork1 = dat1.getTime();
- } catch (ParseException e) {
- e.printStackTrace();
- }
- cc.InsertData(dateWork1, table[0], table[1], table[2], id, "OK", "OK", newprotein, seqs);
- ++countinsertions;
- // flush every 100 insertions
- if (0 == countinsertions % 100) {
- cc.flushData();
- }
- }
- } catch (IOException e) {
- e.printStackTrace();
- }
- } else {
- countNoData++;
- }
+ String[] job = line.split("\\s+");
+ String jobid = job[job.length - 1];
+ if (cw.JobisNotInsterted(jobid)) {
+ countinsertions += analyseJob(job);
} else {
++countinserted;
}
} else {
- if (line.matches(date + "(.*)Sequence0/(.*)")) {
- ++counAlignments;
- } else {
- ++countStrange;
- }
+ ++countNotanalyzed;
}
}
alljobs.close();
System.out.println("Total number of jobs = " + totalcount);
System.out.println(" " + countinserted + " jobs inserted already");
- System.out.println(" " + counAlignments + " jalview jobs");
- System.out.println(" " + countStrange + " not analysed jobs");
- System.out.println(" " + countNoData + " jobs without *.concise.fasta file");
- System.out.println(" " + countUnclearFASTAid + " jobs with unclear FASTA protein id in *.concise.fasta");
+ System.out.println(" " + countNotanalyzed + " not analysed jobs");
+ System.out.println(" " + countNoData + " jobs without *.concise.fasta file (RUNNING or FAILED)");
System.out.println(" " + countinsertions + " new job insertions\n");
} catch (MalformedURLException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
+ ;
}
}
git://source.jalview.org / proteocache.git / blobdiff